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Background <p>Plastid genomes (plastomes) in land plants typically retain a conserved quadripartite structure; yet some angiosperm lineages exhibit extensive structural instability and accelerated sequence evolution. Here, we present a comparative plastome analysis of six species from the subgenus <i>Lychnis</i> (genus <i>Silene</i>, Caryophyllaceae) integrated with previously published plastomes. </p> Results <p>We identify eight large-scale inversions, three independent shifts of the inverted-repeat (IR) boundary, and a marked proliferation of dispersed repeats, implicating repeat-mediated recombination and altered recombination control in driving plastome reorganization. Gene content varied among <i>Lychnis</i> species, including the loss or pseudogenization of <i>accD</i>, <i>infA</i>, and <i>rpl23</i>. Transcriptome data reveal nuclear-encoded homologues with chloroplast-targeting signals, indicating functional replacement via plastid-to-nucleus gene transfer and recruitment of pre-existing nuclear paralogues. Plastid phylogenomic analyses recover the subgenus <i>Lychnis</i> as a strongly supported, monophyletic and early-diverging lineage within the genus <i>Silene</i>, showing that structural changes and substitution rate acceleration have arisen independently of those in other subgenera. Across the genus, synonymous and nonsynonymous substitution rates are elevated in a subset of non-photosynthetic genes, including <i>accD</i> and <i>clpP</i>, with lineage-specific episodes of positive selection detected on several branches.</p> Conclusions <p>Together, these results point to a complex interplay between recombination dynamics, shifts in selective regime and plastid–nuclear interactions, and underscore plastome instability as an important driver of genome evolution within <i>Silene</i> and more broadly across angiosperms.</p>

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Structural variation and evolutionary dynamics of plastid genomes in the subgenus Lychnis (Silene, Caryophyllaceae): insights from genome rearrangements and substitution rates

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  • 发表日期：

    2026年1月14日

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  • Seongjun Park,
  • Ogyeong Son

摘要

Background

Plastid genomes (plastomes) in land plants typically retain a conserved quadripartite structure; yet some angiosperm lineages exhibit extensive structural instability and accelerated sequence evolution. Here, we present a comparative plastome analysis of six species from the subgenus Lychnis (genus Silene, Caryophyllaceae) integrated with previously published plastomes.

Results

We identify eight large-scale inversions, three independent shifts of the inverted-repeat (IR) boundary, and a marked proliferation of dispersed repeats, implicating repeat-mediated recombination and altered recombination control in driving plastome reorganization. Gene content varied among Lychnis species, including the loss or pseudogenization of accD, infA, and rpl23. Transcriptome data reveal nuclear-encoded homologues with chloroplast-targeting signals, indicating functional replacement via plastid-to-nucleus gene transfer and recruitment of pre-existing nuclear paralogues. Plastid phylogenomic analyses recover the subgenus Lychnis as a strongly supported, monophyletic and early-diverging lineage within the genus Silene, showing that structural changes and substitution rate acceleration have arisen independently of those in other subgenera. Across the genus, synonymous and nonsynonymous substitution rates are elevated in a subset of non-photosynthetic genes, including accD and clpP, with lineage-specific episodes of positive selection detected on several branches.

Conclusions

Together, these results point to a complex interplay between recombination dynamics, shifts in selective regime and plastid–nuclear interactions, and underscore plastome instability as an important driver of genome evolution within Silene and more broadly across angiosperms.